Suresh Patel, J. | bioRxiv Science

bioRxiv2024

Exploring the ability of the MD+FoldX method to predict SARS-CoV-2 antibody escape mutations using large-scale data

Antibody escape mutations pose a significant challenge to the effectiveness of vaccines and antibody-based therapies. The ability to predict these escape mutations with computer simulations would allow us to detect threats early and develop effective countermeasures, but a lack of large-scale experimental data has hampered the validation of these calculations. In this study, we evaluate the ability of the MD+FoldX molecular modeling method to predict escape mutations by leveraging a large deep mutational scanning dataset, focusing on the SARS-CoV-2 receptor binding domain. Our results show a positive correlation between predicted and experimental data, indicating that mutations with reduced predicted binding affinity correlate moderately with higher experimental escape fractions. We also demonstrate that better performance can be achieved using affinity cutoffs tailored to distinct antibody-antigen interactions rather than a one-size-fits-all approach. We find that 70% of the systems surpass the 50% precision mark, and demonstrate success in identifying mutations present in significant variants of concern and variants of interest. Despite promising results for some systems, our study highlights the challenges in comparing predicted and experimental values. It also emphasizes the need for new binding affinity methods with improved accuracy that are fast enough to estimate hundreds to thousands of antibody-antigen binding affinities.

biophysics↗

bioRxiv2016

Adaptive mutations in RNA polymerase and the transcriptional terminator Rho have similar effects on Escherichia coli gene expression

Modifications to transcriptional regulators play a major role in adaptation. Here we compared the effects of multiple beneficial mutations within and between Escherichia coli rpoB, the gene encoding the RNA polymerase {beta} subunit, and rho, which encodes a transcriptional terminator. These two genes have harbored adaptive mutations in numerous E. coli evolution experiments but particularly in our previous large-scale thermal stress experiment, where the two genes characterized two alternative adaptive pathways. To compare the effects of beneficial mutations, we engineered four advantageous mutations into each of the two genes and measured their effects on fitness, growth, gene expression and transcriptional termination at 42.2{degrees}C. Among the eight mutations, two rho mutations had no detectable effect on relative fitness, suggesting they were beneficial only in the context of epistatic interactions. The remaining six mutations had an average relative fitness benefit of [~]20%. The rpoB mutations altered the expression of [~]1700 genes; rho mutations altered the expression of fewer genes, most of which were a subset of the genes altered by rpoB. Across our eight mutants, relative fitness correlated with the degree to which a mutation restored gene expression back to the unstressed, 37.0{degrees}C state. The rho mutations do not enhance transcriptional termination in known rho-terminated regions, but the genome-wide effects of mutations in both genes was to enhance termination. Although beneficial mutations in the two genes did not have identical effects on fitness, growth or gene expression, they acted predominantly through parallel phenotypic effects on gene expression and transcriptional termination.

evolutionary biology↗